inst/scripts/Exp1_R25_prot.R

In samWieczorek/DAPARdata: Data accompanying the DAPAR and Prostar packages

library("MSnbase")
library("DAPAR")

exprsFile <- system.file("extdata", "Exp1_R25_prot.txt", package="DAPARdata")

metadataFile <- system.file("extdata", "samples_Exp1_R25.txt", package="DAPARdata")
metadata = read.table(metadataFile, header=TRUE, sep="\t", as.is=TRUE)

Exp1_R25_prot <- createMSnset(file = exprsFile, 
                              metadata = metadata, 
                              indExpData = 49:54, 
                              colnameForID = 'id', 
                              indexForMetacell = 36:41,
                              logData = TRUE, 
                              replaceZeros = TRUE,
                              pep_prot_data = "protein",
                              proteinId = "Protein_IDs",
                              software = 'maxquant')